ambit2.descriptors

Class MolecularWeight

java.lang.Object

ambit2.descriptors.MolecularWeight

All Implemented Interfaces:

org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor

Direct Known Subclasses:

DerivedMolecularWeightDescriptor

public class MolecularWeight
extends Object
implements org.openscience.cdk.qsar.IMolecularDescriptor

Temporary copied from CDK in order to specify the Carbon 12 atomic mass with the right precision (see CDK bug ID ID: 2794591) IDescriptor based on the weight of atoms of a certain element type. If the wild-card symbol * is specified, the returned value is the molecular weight. If an invalid element symbol is specified, the return value is 0 and no exception is thrown

This descriptor uses these parameters:

Name	Default	Description
elementSymbol	*	If *, returns the molecular weight, otherwise the weight for the given element

Returns a single value named wX where X is the chemical symbol or MW if * is specified as a parameter.

Constructor Summary

Constructors

Constructor and Description
MolecularWeight() Constructor for the WeightDescriptor object.

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer container) Calculate the weight of specified element type in the supplied IAtomContainer.
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
String[]	getParameterNames() Gets the parameterNames attribute of the WeightDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the WeightDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the WeightDescriptor object.
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0) Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(Object[] params) Sets the parameters attribute of the WeightDescriptor object.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MolecularWeight

public MolecularWeight()

Constructor for the WeightDescriptor object.

Method Detail

initialise

public void initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)

Returns a Map which specifies which descriptor is implemented by this class. These fields are used in the map:

• Specification-Reference: refers to an entry in a unique dictionary
• Implementation-Title: anything
• Implementation-Identifier: a unique identifier for this version of this class
• Implementation-Vendor: CDK, JOELib, or anything else

Specified by:

initialise in interface org.openscience.cdk.qsar.IDescriptor

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

setParameters

public void setParameters(Object[] params)
                   throws org.openscience.cdk.exception.CDKException

Sets the parameters attribute of the WeightDescriptor object.

Specified by:

setParameters in interface org.openscience.cdk.qsar.IDescriptor

Parameters:

params - The new parameters value

Throws:

org.openscience.cdk.exception.CDKException - if more than 1 parameter is specified or if the parameter is not of type String

See Also:

getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the WeightDescriptor object.

Specified by:

getParameters in interface org.openscience.cdk.qsar.IDescriptor

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

getDescriptorNames

public String[] getDescriptorNames()

Specified by:

getDescriptorNames in interface org.openscience.cdk.qsar.IDescriptor

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainer container)

Calculate the weight of specified element type in the supplied IAtomContainer.

Specified by:

calculate in interface org.openscience.cdk.qsar.IMolecularDescriptor

Parameters:

container - The AtomContainer for which this descriptor is to be calculated. If 'H' is specified as the element symbol make sure that the AtomContainer has hydrogens.

Returns:

The total weight of atoms of the specified element type

getDescriptorResultType

public org.openscience.cdk.qsar.result.IDescriptorResult getDescriptorResultType()

Returns the specific type of the DescriptorResult object.

The return value from this method really indicates what type of result will be obtained from the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.

Specified by:

getDescriptorResultType in interface org.openscience.cdk.qsar.IMolecularDescriptor

Returns:

an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the WeightDescriptor object.

Specified by:

getParameterNames in interface org.openscience.cdk.qsar.IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the WeightDescriptor object.

Specified by:

getParameterType in interface org.openscience.cdk.qsar.IDescriptor

Parameters:

name - Description of the Parameter

Returns:

An Object whose class is that of the parameter requested